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Xenon in PDB 3tf1: Crystal Structure of An H-Nox Protein From T. Tengcongensis Under 6 Atm of Xenon

Protein crystallography data

The structure of Crystal Structure of An H-Nox Protein From T. Tengcongensis Under 6 Atm of Xenon, PDB code: 3tf1 was solved by M.B.Winter, M.A.Herzik Jr., J.Kuriyan, M.A.Marletta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.81 / 2.04
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 80.128, 130.214, 42.810, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 22.1

Other elements in 3tf1:

The structure of Crystal Structure of An H-Nox Protein From T. Tengcongensis Under 6 Atm of Xenon also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Xenon Binding Sites:

The binding sites of Xenon atom in the Crystal Structure of An H-Nox Protein From T. Tengcongensis Under 6 Atm of Xenon (pdb code 3tf1). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 4 binding sites of Xenon where determined in the Crystal Structure of An H-Nox Protein From T. Tengcongensis Under 6 Atm of Xenon, PDB code: 3tf1:
Jump to Xenon binding site number: 1; 2; 3; 4;

Xenon binding site 1 out of 4 in 3tf1

Go back to Xenon Binding Sites List in 3tf1
Xenon binding site 1 out of 4 in the Crystal Structure of An H-Nox Protein From T. Tengcongensis Under 6 Atm of Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of Crystal Structure of An H-Nox Protein From T. Tengcongensis Under 6 Atm of Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe189

b:30.3
occ:0.74
HB A:VAL48 3.4 26.5 1.0
HE3 A:MET1 3.4 20.7 1.0
HG11 A:VAL48 3.5 17.2 1.0
HB3 A:ASP45 3.5 24.0 1.0
HG3 A:ARG49 3.6 40.7 1.0
HE2 A:MET1 3.6 20.7 1.0
HE3 A:MET137 3.6 23.3 1.0
HG2 A:ARG49 3.6 40.7 1.0
HG12 A:VAL48 3.6 17.2 1.0
HZ2 A:TRP67 3.7 21.3 1.0
O A:ASP45 3.8 26.5 1.0
HA A:ASP45 3.8 23.9 1.0
CE A:MET1 3.8 21.4 1.0
HE1 A:MET1 3.8 20.7 1.0
CG1 A:VAL48 3.9 19.1 1.0
SD A:MET137 3.9 23.7 1.0
NH2 A:ARG49 4.0 53.3 1.0
CZ A:ARG49 4.0 57.0 1.0
HH21 A:ARG49 4.0 49.8 1.0
HE1 A:MET137 4.0 23.3 1.0
CE A:MET137 4.1 18.8 1.0
CG A:ARG49 4.1 43.2 1.0
NE A:ARG49 4.1 53.8 1.0
HE A:ARG49 4.1 51.0 1.0
CB A:VAL48 4.1 28.0 1.0
HZ3 A:TRP9 4.1 21.1 1.0
HH2 A:TRP67 4.1 23.1 1.0
HD3 A:ARG135 4.1 25.9 1.0
CZ2 A:TRP67 4.2 20.3 1.0
CB A:ASP45 4.2 27.3 1.0
HH22 A:ARG49 4.3 49.8 1.0
CA A:ASP45 4.4 25.4 1.0
C A:ASP45 4.4 28.4 1.0
HG2 A:MET137 4.4 19.0 1.0
CH2 A:TRP67 4.5 21.6 1.0
NH1 A:ARG49 4.5 57.8 1.0
CG A:ASP45 4.6 24.2 1.0
H A:ARG49 4.6 21.9 1.0
OD1 A:ASP45 4.6 23.2 1.0
HG21 A:VAL48 4.7 26.1 1.0
HH2 A:TRP9 4.7 25.2 1.0
CZ3 A:TRP9 4.8 21.8 1.0
CG A:MET137 4.8 19.7 1.0
CD A:ARG49 4.8 49.0 1.0
HH12 A:ARG49 4.8 52.5 1.0
N A:ARG49 4.8 23.9 1.0
HB3 A:ARG135 4.8 27.6 1.0
HG13 A:VAL48 4.8 17.2 1.0
HH11 A:ARG49 4.9 52.5 1.0
HA A:ARG49 4.9 24.6 1.0
HB2 A:MET1 4.9 23.1 1.0
CG2 A:VAL48 5.0 25.7 1.0
HE2 A:MET137 5.0 23.3 1.0

Xenon binding site 2 out of 4 in 3tf1

Go back to Xenon Binding Sites List in 3tf1
Xenon binding site 2 out of 4 in the Crystal Structure of An H-Nox Protein From T. Tengcongensis Under 6 Atm of Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of Crystal Structure of An H-Nox Protein From T. Tengcongensis Under 6 Atm of Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe190

b:25.7
occ:0.53
HG21 A:ILE51 3.1 22.0 1.0
HE1 A:PHE52 3.1 19.4 1.0
HG13 A:ILE10 3.2 27.6 1.0
HG13 A:VAL6 3.2 22.9 1.0
HD13 A:ILE51 3.4 27.3 1.0
HG12 A:ILE10 3.5 27.6 1.0
HB2 A:TRP9 3.6 18.7 1.0
HD12 A:LEU13 3.6 23.6 1.0
HG13 A:VAL48 3.7 17.2 1.0
HG12 A:VAL6 3.8 22.9 1.0
CG1 A:ILE10 3.8 31.2 1.0
HD12 A:ILE51 3.8 27.3 1.0
HD11 A:LEU13 3.8 23.6 1.0
CG2 A:ILE51 3.9 21.4 1.0
HB3 A:TRP9 3.9 18.7 1.0
CG1 A:VAL6 3.9 26.0 1.0
HE3 A:TRP9 4.0 21.1 1.0
HG22 A:ILE51 4.0 22.0 1.0
HG22 A:VAL48 4.0 26.1 1.0
CE1 A:PHE52 4.0 19.1 1.0
CD1 A:ILE51 4.1 25.8 1.0
CD1 A:LEU13 4.1 27.0 1.0
HB A:ILE51 4.1 30.9 1.0
CB A:TRP9 4.2 19.8 1.0
HD11 A:ILE10 4.2 33.1 1.0
HZ3 A:TRP31 4.2 32.9 1.0
O A:VAL6 4.2 23.3 1.0
HG11 A:VAL6 4.2 22.9 1.0
HD21 A:LEU26 4.3 24.1 1.0
HD1 A:PHE52 4.3 22.2 1.0
HA A:ILE10 4.3 18.2 1.0
HA A:VAL48 4.3 24.1 1.0
H A:ILE10 4.4 17.3 1.0
HD13 A:LEU13 4.4 23.6 1.0
N A:ILE10 4.5 19.1 1.0
CB A:ILE51 4.5 31.3 1.0
CD1 A:ILE10 4.6 37.3 1.0
HG23 A:ILE51 4.6 22.0 1.0
HH2 A:TRP31 4.6 33.9 1.0
CG1 A:VAL48 4.6 19.1 1.0
CD1 A:PHE52 4.6 23.4 1.0
C A:TRP9 4.8 21.3 1.0
HA A:VAL6 4.8 22.9 1.0
CA A:ILE10 4.8 20.3 1.0
HD11 A:ILE51 4.8 27.3 1.0
CZ3 A:TRP31 4.8 34.8 1.0
CG2 A:VAL48 4.8 25.7 1.0
CE3 A:TRP9 4.9 21.9 1.0
HD22 A:LEU26 4.9 24.1 1.0
CD2 A:LEU26 4.9 25.1 1.0
CB A:ILE10 4.9 25.1 1.0
HG11 A:VAL48 5.0 17.2 1.0
CG1 A:ILE51 5.0 29.2 1.0

Xenon binding site 3 out of 4 in 3tf1

Go back to Xenon Binding Sites List in 3tf1
Xenon binding site 3 out of 4 in the Crystal Structure of An H-Nox Protein From T. Tengcongensis Under 6 Atm of Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 3 of Crystal Structure of An H-Nox Protein From T. Tengcongensis Under 6 Atm of Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe189

b:35.1
occ:0.69
HB B:VAL48 3.3 29.8 1.0
HE3 B:MET1 3.3 22.2 1.0
HG11 B:VAL48 3.4 22.5 1.0
HB3 B:ASP45 3.5 30.7 1.0
HG3 B:ARG49 3.5 53.9 1.0
HG12 B:VAL48 3.6 22.5 1.0
HH21 B:ARG49 3.8 70.6 1.0
HZ2 B:TRP67 3.8 23.3 1.0
HE2 B:MET1 3.8 22.2 1.0
NH2 B:ARG49 3.8 65.6 1.0
CG1 B:VAL48 3.8 24.2 1.0
HE1 B:MET1 3.8 22.2 1.0
CE B:MET1 3.8 23.9 1.0
O B:ASP45 3.8 45.8 1.0
HA B:ASP45 3.9 34.7 1.0
CZ B:ARG49 3.9 65.6 1.0
CB B:VAL48 4.0 31.6 1.0
HD3 B:ARG135 4.0 26.3 1.0
HE B:ARG49 4.0 65.0 1.0
NE B:ARG49 4.1 62.5 1.0
HH22 B:ARG49 4.1 70.6 1.0
HZ3 B:TRP9 4.1 24.2 1.0
HE3 B:MET137 4.1 26.1 1.0
SD B:MET137 4.2 25.9 1.0
HH2 B:TRP67 4.2 24.1 1.0
CB B:ASP45 4.2 33.0 1.0
CZ2 B:TRP67 4.3 26.4 1.0
HE1 B:MET137 4.3 26.1 1.0
HH2 B:TRP9 4.4 25.2 1.0
CA B:ASP45 4.4 38.4 1.0
CE B:MET137 4.5 22.6 1.0
CG B:ARG49 4.5 54.0 1.0
HG21 B:VAL48 4.5 31.8 1.0
NH1 B:ARG49 4.5 64.9 1.0
H B:ARG49 4.5 33.3 1.0
C B:ASP45 4.5 44.1 1.0
CG B:ASP45 4.5 32.2 1.0
CH2 B:TRP67 4.5 26.6 1.0
CZ3 B:TRP9 4.7 27.4 1.0
HG13 B:VAL48 4.7 22.5 1.0
OD1 B:ASP45 4.8 36.6 1.0
HH12 B:ARG49 4.8 69.1 1.0
N B:ARG49 4.8 34.9 1.0
CG2 B:VAL48 4.8 33.3 1.0
CH2 B:TRP9 4.8 27.8 1.0
CD B:ARG49 4.9 60.2 1.0
HG2 B:MET137 4.9 21.2 1.0
HG2 B:ARG49 4.9 53.9 1.0
HH11 B:ARG49 4.9 69.1 1.0
HB2 B:MET1 4.9 27.7 1.0
HB3 B:ARG135 5.0 30.2 1.0
CD B:ARG135 5.0 27.0 1.0

Xenon binding site 4 out of 4 in 3tf1

Go back to Xenon Binding Sites List in 3tf1
Xenon binding site 4 out of 4 in the Crystal Structure of An H-Nox Protein From T. Tengcongensis Under 6 Atm of Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 4 of Crystal Structure of An H-Nox Protein From T. Tengcongensis Under 6 Atm of Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe190

b:34.2
occ:0.40
HE1 B:PHE52 2.9 25.1 1.0
HG21 B:ILE51 3.0 32.2 1.0
HG13 B:ILE10 3.0 34.5 1.0
HG13 B:VAL6 3.0 27.0 1.0
HG12 B:ILE10 3.5 34.5 1.0
HD13 B:ILE51 3.6 35.8 1.0
HG13 B:VAL48 3.6 22.5 1.0
CG1 B:ILE10 3.7 38.3 1.0
HB2 B:TRP9 3.7 21.0 1.0
CE1 B:PHE52 3.7 26.7 1.0
HD12 B:LEU13 3.7 25.5 1.0
HD11 B:LEU13 3.8 25.5 1.0
CG2 B:ILE51 3.8 34.1 1.0
HG22 B:ILE51 3.8 32.2 1.0
CG1 B:VAL6 3.8 30.7 1.0
HD11 B:ILE10 3.8 38.8 1.0
HG12 B:VAL6 3.8 27.0 1.0
HE3 B:TRP9 3.8 21.4 1.0
HD12 B:ILE51 3.9 35.8 1.0
HB3 B:TRP9 3.9 21.0 1.0
HB B:ILE51 3.9 34.9 1.0
HD1 B:PHE52 3.9 21.8 1.0
HG22 B:VAL48 4.0 31.8 1.0
CD1 B:ILE51 4.2 39.0 1.0
CD1 B:LEU13 4.2 29.7 1.0
HG11 B:VAL6 4.2 27.0 1.0
HA B:VAL48 4.2 22.9 1.0
CD1 B:PHE52 4.3 24.1 1.0
CB B:TRP9 4.3 23.1 1.0
CD1 B:ILE10 4.3 44.4 1.0
HD21 B:LEU26 4.3 29.4 1.0
O B:VAL6 4.4 27.1 1.0
CB B:ILE51 4.4 37.7 1.0
HA B:ILE10 4.4 25.6 1.0
H B:ILE10 4.5 22.0 1.0
HD13 B:LEU13 4.5 25.5 1.0
HG23 B:ILE51 4.5 32.2 1.0
N B:ILE10 4.5 23.5 1.0
CG1 B:VAL48 4.6 24.2 1.0
HA B:VAL6 4.6 23.8 1.0
HD12 B:ILE10 4.7 38.8 1.0
CE3 B:TRP9 4.7 24.4 1.0
CA B:ILE10 4.8 27.4 1.0
CG2 B:VAL48 4.8 33.3 1.0
CZ B:PHE52 4.9 22.3 1.0
C B:TRP9 4.9 26.9 1.0
CG1 B:ILE51 4.9 40.2 1.0
CB B:ILE10 4.9 30.6 1.0
HD11 B:ILE51 4.9 35.8 1.0
HZ B:PHE52 4.9 21.5 1.0
HH2 B:TRP31 5.0 53.9 1.0
HG11 B:VAL48 5.0 22.5 1.0

Reference:

M.B.Winter, M.A.Herzik, J.Kuriyan, M.A.Marletta. Tunnels Modulate Ligand Flux in A Heme Nitric Oxide/Oxygen Binding (H-Nox) Domain. Proc.Natl.Acad.Sci.Usa V. 108 E881 2011.
ISSN: ISSN 0027-8424
PubMed: 21997213
DOI: 10.1073/PNAS.1114038108
Page generated: Wed Dec 16 02:40:02 2020

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